I've been to 2 urologists 3 times. It's like any other doctor. They'll have you give a urine sample and then you see the doc, explain the problem and they'll examine your penis in whatever way necessary. I'm not sure what cystitus is, but hopefully it can be taken care of easily.
Hell, I once had to get a cystoscopy, where a small tube with a camera end is run INTO your urethra. Not as painful as it sounds, but scary and uncomfortable.

Ok, let me run this through to you as accurately as I can. First, make sure your doctor uses a flexible tube instead of these really old fashioned straight tubes I've heard from others to be really painful. Very few doctors use the straight tubes just cause they're completely old.
Ok, I went in, layed on my back and took down my pants. The doctor first injected (not by a needle) some anesthesia into my penis to coat my urethra so the as to not feel pain when the tube goes in. When he did, I didn't dare to look because I didn't want to see something I'd regret. As the anesthesia goes in there's a stinging sensation (somewhat uncomfortable, but it's the worst of it) in the tip of your penis. It lasts for about 3 seconds though, and then the doc left me in the room for about 10-15 minutes so the fluid could work its way down my urethra to coat it. He put some kind of metal device to keep my penis pointing upwards (didn't hurt, it's not like, PULLED or anything). I just relaxed and thought of other things.
He came back in and with the assistance of a nurse, he used the cystoscope and began his way into my penis. I didn't feel much, but I felt SOMETHING. As I watched the monitor and saw the inside of my penis I began panting with my eyes very worried. This was more my own nerves than actual physical pain causing it. There is no significant physical pain, just the discomfort of knowing exactly what's going on down there (but there is a funny feeling). If you're a strong person, it won't matter. If you're a little wimpy and sensitive like me, you'll be nervous. The best advice I can give you during what I went through which was like a 3 minute ordeal is to stay as calm as you can.
After wards, it comes out and your groin area is wet with distilled water. You clean up, dress up and go.
Now, when I left the office I felt my penis to be numb, like how your tooth feels after a dentist's appointment. The anesthesia takes a few hours to wear off, and slowly but surely you'll regain normal feeling in your penis. BUT I have to warn you, before the cystoscopy, pee out whatever you may have inside. After I came home and relaxed, about 2 hours went by and I went to urinate. A fairly strong and uncomfortable stinging happened upon urination. Like razor blades running through your urethra. a little bit of urine was left in my urethra but since my penis was still kinda numb, it was difficult to push out myself. I just tried to relax. About 2 more hours later I went to the bathroom again to urinate, and the stinging was about half of what it was before. I didn't pee for the rest of the night, slept and in the morning went to the bathroom and my penis was about 90% normal again. Still a SLIGHT discomfort but the anesthesia had almost completely worn off. Later that day I was fine and normal again.
Good luck to you and I hope you get better.

Vicky....all my Dr did was first pee into the cup and they check it for blood...then depending what your issues are they might send you for a CAT scan...or test the urine for other things, its sent out to a lab for that. If tthose tests dont show anything they might have you get the cystoscopy to look at the bladder as cystitis is a bladder issue.

JMDD, the last thing you'll want to do after a cystoscopy is go back to work. Just go home and relax. As for the stinging after the cysto, I wouldn't be surprised if you still feel it even after you've slept for the night. The stinging may not be from the anesthetic but just a natural reaction your penis has after having something put inside it.